Recommend a pseudotime ordering

This function provides a recommendation of a pseudotime ordering based on the metadata available in the monocle object. The recommendation is done by selecting the subgroup of a metadata column that leads to the highest interquartile range of the pseudotime values (or any criteria the user provides). This is translated as an ordering that has the highest variability.

Usage

get_pseudotime_recommendation(
  monocle_object,
  recommendation_criteria = function(pseudotime_values) {
     max(pseudotime_values) -
    min(pseudotime_values)
 }
)

Arguments

monocle_object

A monocle object.

recommendation_criteria

A function that defines the criteria of determining the best pseudotime ordering. The function should take the pseudotime values as input and return a numeric value. The function should be monotonically increasing. Defaults to a function that returns the interquartile range.

Value

A list that contains the recommended metadata column, the subgroup and the pseudotime values.